Microbiota modulation with fermented soy milk - lean vs obese (Diogo Vieira)
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40878 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4695230_1.fastq.gz | Fastqsanger.gz | |||
| ERR4695230_2.fastq.gz | Fastqsanger.gz | |||
| ERR4695240_1.fastq.gz | Fastqsanger.gz | |||
| ERR4695240_2.fastq.gz | Fastqsanger.gz | |||
| ERR4695250_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 120 |
Similar Datasets
Project description:To understand the complex mechanism of estrogen action, multiple assays based on different biological principles is important. Here, multiple assays based on cell, protein and transcription assays were used to evaluate estrogenic activity of soymilk extracts before and after fermentation, and four soy compounds, genistein and daidzein, and their glycosides, genistin and daidzin, respectively. The data obtained by a transcription assay, RNA-sequencing (RNA-seq), was further examined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis to understand cell functions, i.e. biological processes and metabolic pathways. Among the cell functions identified, the sets of genes for cell division/cell cycle and DNA replication/DNA repair are significantly up-regulated, whereas those for autophagy are significantly down-regulated, which explains well the enhanced activity of cell proliferation by these materials. The applications of estrogenic activity of soymilk extracts and soy flavonoids, and the contribution of fermentation, include pharmacological benefits, such as bone protection/bone regeneration, cancer chemoprevention, neuroprotection and the treatment of menopausal syndromes.
2023-10-31 | GSE226627 | GEO
Project description:The study aimed to investigate molecular signatures in peripheral blood of individuals affected by metabolic syndrome (MetS) and different degrees of obesity. Metabolic health of 1204 individuals was assessed, and 32 subjects were recruited to four study groups: MetS lean, MetS obese, “healthy obese” and healthy lean. Whole-blood transcriptome next generation sequencing with functional data analysis was carried out.
2020-02-18 | GSE145412 | GEO
Project description:Soy-based diets have triggered the interest of the research community due to their beneficial effects on a wide variety of pathologies like breast and prostate cancer, diabetes, and atherosclerosis. However, the molecular details underlying these effects are far from being completely understood and several recent attempts have been made to elucidate the soy-induced liver transcriptome changes in different animal models. Here we used Next Generation Sequencing to identify a set of two microRNAs specifically modulated by short-term soy-enriched diet in young male mice and estimate their impact on the liver transcriptome assessed by microarray. Clustering and topological community detection (CTCD) network analysis of STRING generated interactions of transcriptome data led to the identification of five topological communities of genes characteristically altered and putatively targeted by microRNAs upon soy diet intervention.
2018-04-25 | GSE113598 | GEO
Project description:Soy-based diets have triggered the interest of the research community due to their beneficial effects on a wide variety of pathologies like breast and prostate cancer, diabetes, and atherosclerosis. However, the molecular details underlying these effects are far from being completely understood and several recent attempts have been made to elucidate the soy-induced liver transcriptome changes in different animal models. Here we used Next Generation Sequencing to identify a set of two microRNAs specifically modulated by short-term soy-enriched diet in young male mice and estimate their impact on the liver transcriptome assessed by microarray. Clustering and topological community detection (CTCD) network analysis of STRING generated interactions of transcriptome data led to the identification of five topological communities of genes characteristically altered and putatively targeted by microRNAs upon soy diet intervention.
2018-03-15 | GSE111804 | GEO
Project description:Adipose tissue stromal cells contribute to the regulation of adipose tissue in lean and obese states. Myeloid cells such as adipose tissue macrophages (ATMs) and dendritic cells (ATDCs) undergo both quantitative and qualitative changes with obesity. Due to similarity in markers the identify of adipose tissue dendritic cells and macrophages has been elusive. We have refined prior protocols to unambiguously discern ATM and ATDC in mice. We used microarrays to compare the profiles of ATMs and ATDC from gonadal adipose tissue from lean, obese, and formerly obese mice. We also isolated preadipocytes (PA) from lean and obese mice for comparison. Male C57Bl/6 mice were fed normal diet (ND) or high fat diet (HFD) for 16 weeks. Weight loss (WL) mice were switched from the HFD to ND for 8 weeks. RNA was purified from FACS sorted cell populations (live cells only) obtained from gonadal/epididymal adipose tissue depots. ATMs were defined as CD11c+ (CD45+CD64+ CD11c+) or CD11c- (CD45+CD64+ CD11c-) ATMs. ATDC were defined as CD64- CD11c+. PA were defined as CD31- CD45- Sca1+ PDGFRA+.
2016-09-01 | GSE85846 | GEO
Project description:Obtaining adipose tissue samples are paramount to the understanding of human obesity. We have examined the impact of needle-aspirated and surgical biopsy techniques on the study of subcutaneous adipose tissue (scAT) gene expression in both obese and lean subjects. Biopsy sampling methods have a significant impact on data interpretation and revealed that gene expression profiles derived from surgical tissue biopsies better capture the significant changes in molecular pathways associated with obesity. We hypothesize that this is because needle biopsies do not aspirate the fibrotic fraction of scAT; which subsequently results in an under-representation of the inflammatory and metabolic changes that coincide with obesity. This analysis revealed that the biopsy technique influences the gene expression underlying the biological themes commonly discussed in obesity (e.g. inflammation, extracellular matrix, metabolism, etc), and is therefore a caveat to consider when designing microarray experiments. These results have crucial implications for the clinical and physiopathological understanding of human obesity and therapeutic approaches. Keywords: subject and tissue biopsy technique comparison Tissue samples from lean and obese subjects were analyzed: total of 36 hybridizations. The goal was to compare the effect of biopsy sampling methods on global subcutaneous adipose tissue gene expression analyses. The following subject groups were used for the analysis: 9 lean subjects: needle biopsy 9 lean subjects: surgical biopsy 9 obese subjects: needle biopsy 9 obese subjects: surgical biopsy
2008-12-22 | E-GEOD-12050 | biostudies-arrayexpress
Project description:We did single cell RNA sequencing on three lean and three obese donors. For each donor, we sorted CD45 positive and CD45 negative cells and prepared 10X scRNA-seq libaries. We observed cell type compositon changes and expression changes in the lean and obese donors.
2021-03-09 | GSE155960 | GEO
Project description:Objective: The etiology of PCOS is mostly unknown. Existing data support both genetic and environmental factors in its pathogenesis. Design: Prospective case - control study. Setting: University Hospital. Patients: 25 patients undergoing IVF-ICSI treatment. Intervention: Genome-wide oligonucleotide microarray technology was used to study differential gene-expression patterns of cultured human cumulus cells from IVF patients divided into 4 groups according to disease state (PCOS vs. Control) and BMI (Obese vs. Lean). Results: Two differential PCOS gene expression profiles were established: Lean-Type was formed by comparing PCOS lean (PL) vs. non-PCOS lean (NL) individuals; Obese-Type was formed by comparing PCOS obese (PO) vs. non-PCOS (NO) obese patients. Conclusions: Different molecular pathways are associated with PCOS in Lean and Obese individuals, as demonstrated by gene expression profiling of cumulus cells. Our findings provide insights into the molecular pathogenesis of PCOS. We used microarrays to study the gene expression of human cultured cumulus cells. We compared the genes expression of lean PCOS, Obese PCOS, lean controls and obese controls. Different molecular pathways are associated with PCOS in Lean and Obese patients. Experiment Overall Design: Cumulus cells obtained from woman undergoing IVF/ICSI. Following oocyte retrieval, cumulus cells were stripped from the oocyte, in preparation for the ICSI process, with a micropipette. After 48h in culture the cumulus cells were collected for RNA extraction and hybridization on Affymetrix microarrays. We compered the expression profile of 4 groups - lean PCOS, obese PCOS, lean controls and obese controls.
2008-06-11 | E-GEOD-10946 | biostudies-arrayexpress
Project description:To figure out how obesity drives glycolysis in CD4+ T cells, we performed RNA-sequencing to analyze the transcriptome of lean and obese-derived splenic CD4+ T cells. Mice were fed with either a normal diet (referred to lean mice) or a high-fat diet (HFD, 60 kcal% fat, referred to obese mice) generally from 6-8 weeks of age, for up to 4 months.
2023-01-11 | GSE188864 | GEO
Project description:Background There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy supplementation on breast cancer-related genes and pathways. Methods Women (n = 140) with early-stage breast cancer were randomized to soy protein supplementation (n = 70) or placebo (n = 70) for 7 to 30 days, from diagnosis until surgery. Adherence was determined by plasma isoflavones: genistein and daidzein. Gene expression changes were evaluated by NanoString inin pre- and post-treatment tumor tissue. Genome-wide expression analysis was performed on post-treatment tissue. Proliferation (Ki67) and apoptosis (Cas3) were assessed by immunohistochemistry. Results Plasma isoflavones rose in the soy group (two-sided Wilcoxon rank-sum test, P < .001) and did not change in the placebo group. In paired analysis of pre- and post-treatment samples, 21 genes (out of 202) showed altered expression (two-sided Student’s t-test, P < .05). Several genes including FANCC and UGT2A1 revealed different magnitude and direction of expression changes between the two groups (two-sided Student’s t-test, P < .05). A high-genistein signature consisting of 126 differentially expressed genes was identified from microarray analysis of tumors. This signature was characterized by overexpression (>2 fold) of cell cycle transcripts, including those which promote cell proliferation, such as FGFR2, E2F5, BUB1, CCNB2, MYBL2, CDK1, and CDC20 (P < .01). Soy intake did not result in statistically significant changes in Ki67 or Cas3. Conclusions Gene expression associated with soy intake and high plasma genistein define a signature characterized by overexpression of FGFR2 and genes that drive cell cycle and proliferation pathways. These findings raise the concerns that in a subset of women soy could adversely affect gene expression in breast cancer.
2014-07-01 | GSE58792 | GEO